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source("tianfengRwrappers.R")
载入需要的程辑包:reticulate
载入需要的程辑包:tidyr
载入程辑包:‘MySeuratWrappers’
The following objects are masked from ‘package:Seurat’:
DimPlot, DoHeatmap, LabelClusters, RidgePlot, VlnPlot
载入程辑包:‘ggpubr’
The following object is masked from ‘package:rbokeh’:
set_palette
载入程辑包:‘cowplot’
The following object is masked from ‘package:ggpubr’:
get_legend
载入需要的程辑包:viridisLite
载入程辑包:‘reshape2’
The following object is masked from ‘package:tidyr’:
smiths
NOTE: Either Arial Narrow or Roboto Condensed fonts are required to use these themes.
Please use hrbrthemes::import_roboto_condensed() to install Roboto Condensed and
if Arial Narrow is not on your system, please see https://bit.ly/arialnarrow
clusterProfiler v3.14.3 For help: https://guangchuangyu.github.io/software/clusterProfiler
If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
Registering fonts with R
载入程辑包:‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:stats’:
filter
The following object is masked from ‘package:graphics’:
layout
载入需要的程辑包:e1071
Registered S3 methods overwritten by 'proxy':
method from
print.registry_field registry
print.registry_entry registry
载入程辑包:‘widgetTools’
The following object is masked from ‘package:dplyr’:
funs
载入程辑包:‘DynDoc’
The following object is masked from ‘package:BiocGenerics’:
path
载入程辑包:‘IDPmisc’
The following object is masked from ‘package:shiny’:
hr
载入程辑包:‘DT’
The following objects are masked from ‘package:shiny’:
dataTableOutput, renderDataTable
The following object is masked from ‘package:Seurat’:
JS
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circlize version 0.4.13
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
in R. Bioinformatics 2014.
This message can be suppressed by:
suppressPackageStartupMessages(library(circlize))
========================================
载入需要的程辑包:grid
========================================
ComplexHeatmap version 2.2.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
载入程辑包:‘ComplexHeatmap’
The following object is masked from ‘package:plotly’:
add_heatmap
BMP相关基因
gsave("BMPreceptor_ds1.png", device = png, plot = Dotplot(c("BMPR1A","BMPR1B"),ds1), height = 6, width = 5)
Error in gsave("BMPreceptor_ds1.png", device = png, plot = Dotplot(c("BMPR1A", :
没有"gsave"这个函数
library(fmsb)
data <- read.csv("./go_res.csv",row.names = 1,quote = "", check.names=FALSE)
# data=as.data.frame(matrix(sample(0:50, 18,replace=T) , ncol=6))
# colnames(data)=c('IL-1 signaling pathway','Response to IFNa','NFkB signaling pathway','IL-6 signaling pathway', 'Muscle contraction','Response to IFNr')
# rownames(data) <- c('Monocyte','Neutrophil','Macrophage')
# 用于生成雷达图的最大最小值
data=rbind(rep(15,5) , rep(-10,5) , data)
colors_border <- colors_list[c(4,1,5)]
colors_in <- aero_colors_list[c(4,1,5)]
svg("GO_res.svg",height = 8,width = 10)
radarchart(data, axistype=0, seg = 5,
pcol=colors_border, pfcol=colors_in, plwd=1.3 , plty=1,pty=32,
cglcol="black", cglty=3, cglwd=0.6,
)
legend(x=-1.6, y=0.5, legend = rownames(data[-c(1,2),]), bty = "n", pch=20 , col=colors_border, text.col = "black", cex=1, pt.cex=2)
dev.off()
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